There's a checkbox to active/deactivate the feature "Do not remove any file on the NAS during synchronization".
Currently, this is a general setting that is applied across any paired folders and all folder/files within.

I can't imagine, that I'm the only one who'd like to have more granular control over this.
I'd like to be able to:

Activate/Deactivate "Smart Delete" for each paired folder separately

Activate/Deactivate "Smart Delete" for each folder within a paired folder

Hopefully, QNAP will consider this as a useful enhancement and will implement it soon.